--- license: apache-2.0 task_categories: - text-generation tags: - biology - genomics - dna - benchmark configs: - config_name: motif_human data_files: - split: test path: motif_human/test-* - config_name: syn_human data_files: - split: test path: syn_human/test-* - config_name: syn_mouse data_files: - split: test path: syn_mouse/test-* dataset_info: - config_name: syn_human features: - name: benchmark_id dtype: string - name: script_version dtype: string - name: annotation_source dtype: string - name: genome_assembly dtype: string - name: codon_usage_source dtype: string - name: recoding_mode dtype: string - name: optimization_rate dtype: float64 - name: random_seed dtype: int64 - name: window_size_bp dtype: int64 - name: species dtype: string - name: chr dtype: string - name: chrom_length dtype: int64 - name: strand dtype: string - name: cds_genome_start dtype: int64 - name: cds_genome_end dtype: int64 - name: window_genome_start dtype: int64 - name: window_genome_end dtype: int64 - name: upstream_actual dtype: int64 - name: downstream_actual dtype: int64 - name: is_clamped dtype: int64 - name: transcript_id dtype: string - name: gene_id dtype: string - name: gene_name dtype: string - name: exon_rank dtype: int64 - name: is_first_exon dtype: int64 - name: frame dtype: int64 - name: phase_gtf dtype: int64 - name: cds_start_in_seq dtype: int64 - name: cds_end_in_seq dtype: int64 - name: cds_length dtype: int64 - name: patch_start_in_seq dtype: int64 - name: patch_end_in_seq dtype: int64 - name: patch_length dtype: int64 - name: n_codons_total dtype: int64 - name: n_codons_eligible dtype: int64 - name: n_codons_changed dtype: int64 - name: fraction_codons_changed dtype: float64 - name: original_sequence dtype: string - name: sequence dtype: string splits: - name: test num_bytes: 335904126 num_examples: 20000 download_size: 152737063 dataset_size: 335904126 - config_name: syn_mouse features: - name: benchmark_id dtype: string - name: script_version dtype: string - name: annotation_source dtype: string - name: genome_assembly dtype: string - name: codon_usage_source dtype: string - name: recoding_mode dtype: string - name: optimization_rate dtype: float64 - name: random_seed dtype: int64 - name: window_size_bp dtype: int64 - name: species dtype: string - name: chr dtype: string - name: chrom_length dtype: int64 - name: strand dtype: string - name: cds_genome_start dtype: int64 - name: cds_genome_end dtype: int64 - name: window_genome_start dtype: int64 - name: window_genome_end dtype: int64 - name: upstream_actual dtype: int64 - name: downstream_actual dtype: int64 - name: is_clamped dtype: int64 - name: transcript_id dtype: string - name: gene_id dtype: string - name: gene_name dtype: string - name: exon_rank dtype: int64 - name: is_first_exon dtype: int64 - name: frame dtype: int64 - name: phase_gtf dtype: int64 - name: cds_start_in_seq dtype: int64 - name: cds_end_in_seq dtype: int64 - name: cds_length dtype: int64 - name: patch_start_in_seq dtype: int64 - name: patch_end_in_seq dtype: int64 - name: patch_length dtype: int64 - name: n_codons_total dtype: int64 - name: n_codons_eligible dtype: int64 - name: n_codons_changed dtype: int64 - name: fraction_codons_changed dtype: float64 - name: original_sequence dtype: string - name: sequence dtype: string splits: - name: test num_bytes: 336064778 num_examples: 20000 download_size: 152659316 dataset_size: 336064778 - config_name: motif_human features: - name: benchmark_id dtype: string - name: script_version dtype: string - name: annotation_source dtype: string - name: genome_assembly dtype: string - name: upstream_flank_bp dtype: int64 - name: motif dtype: string - name: actual_motif dtype: string - name: patch_len_bp dtype: int64 - name: start_after_bp dtype: int64 - name: random_seed dtype: int64 - name: species dtype: string - name: chr dtype: string - name: chrom_length dtype: int64 - name: strand dtype: string - name: cds_genome_start dtype: int64 - name: cds_genome_end dtype: int64 - name: window_genome_start dtype: int64 - name: window_genome_end dtype: int64 - name: upstream_actual dtype: int64 - name: is_clamped dtype: int64 - name: transcript_id dtype: string - name: gene_id dtype: string - name: gene_name dtype: string - name: exon_rank dtype: int64 - name: is_first_exon dtype: int64 - name: frame dtype: int64 - name: phase_gtf dtype: int64 - name: cds_start_in_seq dtype: int64 - name: cds_end_in_seq dtype: int64 - name: cds_length dtype: int64 - name: patch_start_in_cds dtype: int64 - name: patch_end_in_cds dtype: int64 - name: patch_start_in_seq dtype: int64 - name: patch_end_in_seq dtype: int64 - name: original_sequence dtype: string - name: sequence dtype: string splits: - name: test num_bytes: 334784354 num_examples: 20000 download_size: 152132105 dataset_size: 334784354 --- # Carbon Perturbation Bench A benchmark of **sequence-level perturbation tasks** for evaluating DNA foundation models. Each task presents pairs of genomic sequences — one real (unperturbed) and one structurally altered — and asks whether the model assigns higher log-likelihood to the original. **Metric**: pairwise discrimination accuracy = `mean(LL(original) > LL(perturbed))` --- ## Tasks ### `syn_human` · `syn_mouse` — Synonymous codon substitution (20,000 pairs each) Codons within a real CDS are replaced with the highest-frequency synonym for the target species (`recoding_mode = "optimize"`, `optimization_rate = 1.0`), while the upstream and downstream flanking sequence is left unchanged. Amino acid identity is preserved by construction. The model should prefer the natural codon usage over the artificially optimised variant. - **Human** (`syn_human`): GENCODE v45 annotations on GRCh38/hg38; codon frequencies from CoCoPUTs (*H. sapiens* RefSeq CDS); 9,616 unique genes. - **Mouse** (`syn_mouse`): GENCODE vM34 annotations on GRCm39/mm39; codon frequencies from CoCoPUTs (*M. musculus* RefSeq CDS); 10,253 unique genes. - Window size: 8,192 bp centred on the CDS (`cds_start_in_seq` / `cds_end_in_seq`). - Mean fraction of codons changed: ~55% (range 10–95%). ### `motif_human` — CAG repeat insertion (20,000 pairs) A 30 bp region starting 60 bp downstream of the CDS start is replaced with 10 consecutive CAG triplets (`CAGCAGCAGCAGCAGCAGCAGCAGCAGCAG`), mimicking the pathological trinucleotide repeat expansions underlying polyglutamine disorders (Huntington's disease, SCAs, DRPLA). The substitution is length-preserving (30 bp in, 30 bp out), so the total window remains 8,192 bp. All sequence outside the patch is identical between original and perturbed. - Annotations: GENCODE v45 / GRCh38; 9,705 unique genes. - Window layout: 8,102 bp upstream flank, CDS start at position 8,102, patch at positions 8,162–8,192. --- ## Schema All configs share the key columns: | Column | Description | |---|---| | `original_sequence` | Real, unperturbed genomic sequence — **positive** | | `sequence` | Structurally altered sequence — **negative** | | `cds_start_in_seq` / `cds_end_in_seq` | CDS boundaries within the window (bp offset) | | `chr`, `strand` | Genomic locus | | `gene_name`, `transcript_id` | GENCODE annotation | | `benchmark_id` | Unique row identifier | Config-specific columns (e.g. `patch_start_in_seq`, `n_codons_changed`, `fraction_codons_changed`, `codon_usage_source`) are described in the dataset info above. --- ## Usage ```python from datasets import load_dataset # Synonymous codon substitution — human syn_human = load_dataset( "HuggingFaceBio/carbon-perturbation-bench", "syn_human", split="test" ) # Synonymous codon substitution — mouse syn_mouse = load_dataset( "HuggingFaceBio/carbon-perturbation-bench", "syn_mouse", split="test" ) # CAG motif insertion motif = load_dataset( "HuggingFaceBio/carbon-perturbation-bench", "motif_human", split="test" ) ``` --- ## Evaluation A ready-to-run scorer for Carbon, GENERator, and Evo2 is available at [`evaluation/perturbation_tasks.py`](https://github.com/huggingface/carbon) in the Carbon release repository. ```bash python evaluation/perturbation_tasks.py \ --task syn_human \ --model HuggingFaceBio/Carbon-3B \ --bf16 python evaluation/perturbation_tasks.py \ --task motif_human \ --model arcinstitute/evo2_7b --backend evo2 \ --bf16 ```